Classification of Databases

A strict separation of these three types of databases is difficult hence most databases contain a mixture of data types. Therefore the classification given here is based on the predominating data type. For example, the major emphasis of a patent database is on hterature, whereas it also comprises numeric and structural data. Another type is the integrated database, which provides a supplement of additional information, especially bibhographic data. Thus, different database types are merged, a textual database and one or more factual databases. 

One of the more prominent integrated databases is provided by CAS - the Registry CAPLUS, CA, CAOLD. All of these diverse databases are based on the 

Nedaork model more efficit nt than relational model better integrity support than relational model miore difficult lo design and 1o use than relational model requires knowledge of data smicfure less data independence than relational model 

Relational model ease of use without in-dcpih knowledge high degree of data independence SQl capability less cflicicnt lhan other miodels integrity problems possible to misuse 

Ohject-bastd model data representation in many differenl data types supports temporal and higher- dimensional data objecis can be reused difficull to design DHMS slow perfonnanee 

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The user is often more interested in the contents than in the technical organization of databases. The wide variety of data allows the classification of databases in chemistry into literature, factual (alphanumeric), and structural types (Figure 5-10) [12, 13). 

Classifications of databases are often found but they reflect the point of view of the author. According to Warr and Suhr databases in chemistry may be classified as follows ... 

It is clear that in some cases the classification of databases is not as simple as suggested by this scheme. Consider for... 

To become familiar with the classification of chemical databases according to their data content... 

More elaborate scheme.s can he envisaged. Thus, a. self-organizing neural network as obtained by the classification of a set of chemical reactions as outlined in Section 3,5 can be interfaced with the EROS system to select the reaction that acmaliy occurs from among various reaction alternatives. In this way, knowledge extracted from rcaetion databases can be interfaced with a reaction prediction system,... 

SCOP Structural Classification of Proteins. Hierarchical protein structure database... 

Murzin A G, S E Brenner, T Hubbard and C Chothia 1995. SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247 536-540. 

TJP Hubbard, B Alley, SE Brenner, AGMurzm, C Chothia. SCOP A stiaictural classification of proteins database. Nucleic Acids Res 27 254-256, 1999. 

Sequence conservation is, in general, much weaker than structural conservation. There are proteins, which are clearly not related in sequence but are closely related in 3D-stmcture and fold, like heamoglobin and myoglobin, which have similar functions. In many proteins, fold elements like 4-helical bundles are repeated. Classifications of known structural folds of proteins are organized in the SCOP or CATH database see e.g., http //scop.mrc-lmb.cam.ac.uk/scop/. 

Tatusov RL, Natale DA, Garkavtsev IV et al. The COG database new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001 29[l] 22-28. 

Selected entries from Methods in Enzymology [vol, page(s)] General Protein kinase classification, 200, 3 protein kinase catalytic domain sequence database identification of conserved features of primary structure and classification of family members,... 

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